Introduction: Gestational diabetes mellitus (GDM) is a significant public health concern, due to its association with short- and long-term complications in both mothers and offspring. DNA methylation and single nucleotide polymorphisms (SNPs) offer potential to serve as molecular biomarkers, which may lead to improved detection of GDM with positive effects on health outcomes. Aim: The aim of this study was to investigate whether DNA methylation and SNPs are associated with GDM and may offer potential as molecular biomarkers for GDM in South Africa (SA). Methods: This study followed a two-pronged approach. Firstly, literature searches were conducted to collate and synthesise all published articles reporting on the prevalence of GDM in SA, the screening and diagnostic strategies used, and the current status of DNA methylation and SNPs as biomarkers for GDM. Secondly, we conducted experiments to investigate global (n=201), genome-wide (n=24) and gene-specific DNA methylation (n=286) of the adiponectin gene (ADIPOQ) in whole blood of women with and without GDM, using an Enzyme-Linked Immunosorbent Assay, a methylationEPIC BeadChip Array and pyrosequencing, respectively. In addition, genotype and allele frequencies of ADIPOQ rs266729 and rs17300539, and methylenetetrahydrofolate reductase (MTHFR) rs1801133 were determined, using quantitative real-time PCR (n=449) and DNA sequencing for validation. Results: The literature search showed that the prevalence of GDM in SA has increased over the years. Furthermore, it showed that the lack of uniformity in screening and diagnosis between and within countries hamper the accurate detection of GDM. Lastly, the literature search identified several studies that support the use of DNA methylation and SNPs as potential biomarkers for GDM. Experimentally, we showed no differences in global DNA methylation between GDM and non-GDM groups. Interestingly, global DNA methylation levels were 18% (p=0.012) higher in obese compared to non-obese pregnant women. Genome-wide methylation analysis identified 1046 differentially methylated CpG sites (associated with 939 genes) (Cut-off threshold: M>0.06 and p<0.01). Among the top five CpG sites identified, one CpG mapped to the calmodulin-binding transcription activator 1 (CAMTA1) gene, which has been shown to regulate insulin production and secretion. Two CpG sites (-3410: p=0.048 and -3400: p=0.004) in the ADIPOQ promoter were hypomethylated during GDM in HIV negative, but not in HIV positive women. Lastly, no association between the ADIPOQ and MTHFR polymorphisms and GDM was observed in our population. Conclusion: To our knowledge, this is the first study to investigate the association between DNA methylation or ADIPOQ (rs266729 and rs17300539) and MTHFR (rs1801133) polymorphisms and GDM in SA. Findings suggest that gene-specific, but not global methylation nor SNPs rs266729, rs17300539 and rs1801133, may offer potential as molecular biomarkers of GDM in this population. Future longitudinal studies in larger samples that include both HIV negative and positive pregnant women are warranted to explore the candidacy of DNA methylation as molecular biomarkers for GDM. / Thesis (PhD)--University of Pretoria, 2019. / National Research Foundation (NRF) of South Africa, Thuthuka Grant (unique grant no. 99391). / South African Medical Research Council (SAMRC) / Obstetrics and Gynaecology / PhD / Unrestricted

Os marcadores orgânicos moleculares (hidrocarbonetos alifáticos, esteróis e álcoois) em amostras de sedimentos superficiais e de testemunhos curtos coletados em diápiros e pockmarks localizados no talude sul do Brasil, foram utilizados para identificar as possíveis contribuições biogênicas (autóctones / alóctones). De modo geral, tanto nas amostras superficiais como ao longo dos testemunhos, o maior acúmulo de carbono orgânico total nos pockmarks foi observado, indicando o possível aprisionamento de sedimentos e de matéria orgânica no interior das concavidades. A presença de &#946;-sitosterol, campesterol, álcoois e n-alcanos pesados, indicaram contribuições terrígenas para a área de estudo, que pode ser advinda da descarga continental do Rio da Prata, uma vez que a predominância terrígena é proveniente das pradarias, típica vegetação do Uruguai e do sul do Rio Grande do Sul. O transporte de sedimentos terrígenos ocorre em direção ao norte, ao longo da plataforma continental sul brasileira, pela Corrente Costeira do Brasil. A presença de detritos de fitoplâncton e zooplâncton também ocorre devido à influência dos nutrientes do Rio da Prata. As possíveis liberações de gás/fluido, que sustentaram ecossistemas quimiossintéticos em diferentes intervalos de dois testemunhos em pockmark e diápiro foram constatadas através da presença relativamente maior de n-alcanos leves com número par de carbonos. / Organic molecular markers (aliphatic hydrocarbons, sterols and alcohols) in superficial and short cores sediment samples collected in diapirs and pockmarks located in the southern slope of Brazil were used in order to identify the possible biogenic contributions (autochthonous / allochthonous). In general, in surface samples and throughout the cores samples, the greatest accumulation of total organic carbon in the pockmarks was observed, indicating the possible entrapment of sediments and organic matter inside the concavities. The presence of &#946;-sitosterol, campesterol, alcohols and heavy n-alkanes indicated terrigenous contributions to the study area, which may be due to the continental discharge of Río de la Plata, since the terrigenous predominance is due to the prairies, a typical vegetation of Uruguay and the south of Rio Grande do Sul. The terrigenous sediments transport is carried through the North, along the Brazilian continental shelf, by the Coastal Stream of Brazil. The presence of phytoplankton and zooplankton debris is also due to the influence of the nutrients contribution from Río de la Plata. Possible gas / fluid releases, which sustained chemosynthetic ecosystems at different intervals of two pockmark and diaper cores, were verified by the relative predominance of even-numbered carbon n-alkanes.

Os marcadores orgânicos moleculares (hidrocarbonetos alifáticos, esteróis e álcoois) em amostras de sedimentos superficiais e de testemunhos curtos coletados em diápiros e pockmarks localizados no talude sul do Brasil, foram utilizados para identificar as possíveis contribuições biogênicas (autóctones / alóctones). De modo geral, tanto nas amostras superficiais como ao longo dos testemunhos, o maior acúmulo de carbono orgânico total nos pockmarks foi observado, indicando o possível aprisionamento de sedimentos e de matéria orgânica no interior das concavidades. A presença de &#946;-sitosterol, campesterol, álcoois e n-alcanos pesados, indicaram contribuições terrígenas para a área de estudo, que pode ser advinda da descarga continental do Rio da Prata, uma vez que a predominância terrígena é proveniente das pradarias, típica vegetação do Uruguai e do sul do Rio Grande do Sul. O transporte de sedimentos terrígenos ocorre em direção ao norte, ao longo da plataforma continental sul brasileira, pela Corrente Costeira do Brasil. A presença de detritos de fitoplâncton e zooplâncton também ocorre devido à influência dos nutrientes do Rio da Prata. As possíveis liberações de gás/fluido, que sustentaram ecossistemas quimiossintéticos em diferentes intervalos de dois testemunhos em pockmark e diápiro foram constatadas através da presença relativamente maior de n-alcanos leves com número par de carbonos. / Organic molecular markers (aliphatic hydrocarbons, sterols and alcohols) in superficial and short cores sediment samples collected in diapirs and pockmarks located in the southern slope of Brazil were used in order to identify the possible biogenic contributions (autochthonous / allochthonous). In general, in surface samples and throughout the cores samples, the greatest accumulation of total organic carbon in the pockmarks was observed, indicating the possible entrapment of sediments and organic matter inside the concavities. The presence of &#946;-sitosterol, campesterol, alcohols and heavy n-alkanes indicated terrigenous contributions to the study area, which may be due to the continental discharge of Río de la Plata, since the terrigenous predominance is due to the prairies, a typical vegetation of Uruguay and the south of Rio Grande do Sul. The terrigenous sediments transport is carried through the North, along the Brazilian continental shelf, by the Coastal Stream of Brazil. The presence of phytoplankton and zooplankton debris is also due to the influence of the nutrients contribution from Río de la Plata. Possible gas / fluid releases, which sustained chemosynthetic ecosystems at different intervals of two pockmark and diaper cores, were verified by the relative predominance of even-numbered carbon n-alkanes.

Les écosystèmes aquatiques constituent la destination finale des contaminants. Les organismes aquatiques sont ainsi impactés par un cocktail de molécules, dont les produits phytosanitaires. Le caractère perturbateur endocrinien (PE) de certains d’entre eux est particulièrement préoccupant. La présente étude explore les effets de pesticides modèles à potentiel PE – la chlordécone (CLD) et le pyriproxyfène (PXF), seuls et en mélange – chez le copépode estuarien Eurytemora affinis par des approches écotoxicogénomiques innovantes. En réponse aux PE, l’accent a été porté sur les effets de ces composés sur la reproduction, la croissance ou le développement. En parallèle, l’affinité des pesticides aux récepteurs aux oestrogènes et aux androgènes humains d’une part, et aux ecdystéroïdes d’autre part, a été étudiée grâce à des outils bio analytiques afin d’évaluer la pertinence de l’utilisation du potentiel PE défini par les tests cellulaires comme critère d’exclusion dans la réglementation européenne des pesticides. Ces travaux de thèse présentent, pour la première fois, les transcriptomes et protéomes d’E. affinis après exposition aux PE. Un effet sexe-dépendant a été observé par les deux approches « omics » révélant un plus fort impact des composés sur les copépodes mâles. Des gènes et protéines, impliqués dans le processus de mue et dans la gamétogénèse ont été identifiés comme candidats pour le développement de biomarqueurs moléculaires de PE chez les crustacés. Les tests cellulaires ont permis de mettre en évidence des interactions entre les contaminants et les récepteurs hormonaux. Toutefois, le screening de molécules par les tests YES/YAS/anti-YES/anti-YAS s’est heurté à quelques limites d’interprétations. Enfin, les résultats du test S2 EcR, souligne la pertinence de l'utilisation couplée de tests spécifiques d’un système endocrinien de vertébrés et d’invertébrés dans l’évaluation du risque des composés PE. / Aquatic ecosystems constitute the chemicals’ final destination. Among the xenobiotics, endocrine disruptors (ED) are compounds of major concern. In this context, ED pesticides effects were investigated in the widespread copepod Eurytemora Affinis using ecotoxicogenomics technics. In response to PE pesticides, focus was made on reproduction, growth and development. In order to evaluate the endocrine activity, in vitro tests (YES/YAS/anti-YES/anti-YAS and S2 EcR) were used to screen the compounds alone and in mixtures. These results were discussed to evaluate the “cut off criterion” used in European assessment. This work presents for the first time, transcriptomes and proteomes of E. affinis after PXF and CLD –alone and in binary mixture- exposure. A sex dependent effect was observed by the two “omics” approaches. Male copepods were more impacted by contaminants than female copepods. Genes and proteins (e.g. chitin deacetylase, kelch protein) were identified as candidates for the development of ED molecular biomarkers. In vitro tests highlighted binding of pesticides with both vertebrate and invertebrate receptors. However, a toxicity for the highest concentrations tested and some limits for the interpretation of mixtures results were limiting in YES/YAS/anti-YES/anti-YAS assays. The last observation represents particularly a major concern for interpretation of the ED mode of action of environmental matrix. S2 EcR highlighted some complementary results about the mode of action of chemicals alone and in binary mixtures. These results accentuate the need to combine vertebrate specific test and invertebrate specific test in ED risk assessment.

Magister Chirurgiae Dentium (MChD) / Water-pipe tobacco smoking (WTS) is a form of tobacco use with different names. There is a misconception that passing tobacco smoke through water reduces its harmful effects to increase its popularity. One million individuals smoke water-pipe daily, resulting in approximately five million deaths per annum globally. The toxic effects of WTS are related to the several components of the tobacco mixture. WTS contains 100 times more tar, four-fold more nicotine, eleven-fold more Carbon Monoxide (CO), and two to five-fold more polycyclic aromatic hydrocarbons than cigarettes.

Alta prevalência, farmacorresistência e bom prognóstico cirúrgico são algumas das características clínicas que tornam a epilepsia do lobo temporal mesial com esclerose hipocampal (ELTM-EH) uma das mais importantes formas de epilepsia. Ela é o modelo da epilepsia cirurgicamente curável. Infelizmente, cerca de 10% dos pacientes evoluem com resultado cirúrgico insatisfatório. A ELTM-EH está associada a alterações amplas do perfil de expressão dos microRNAs (miRNAs) do hipocampo. Recentemente, constatou-se a existência de miRNAs estáveis no sangue periférico e em outros fluidos corporais, comprovadamente aplicáveis como biomarcadores, cuja abrangência vai do diagnóstico à resposta terapêutica. Tendo isso em vista, a pesquisa partiu do seguinte questionamento: é possível a identificação, no sangue periférico, de assinaturas moleculares por miRNAs que predigam o resultado do tratamento cirúrgico da ELTM-EH? Por meio de técnicas de biologia molecular, avaliaram-se amostras de sangue e hipocampo de pacientes submetidos à lobectomia temporal anterior em consequência de ELTMEH farmacorresistente. As amostras eram representativas de indivíduos com resultado cirúrgico favorável (Engel IA) e desfavorável (Engel III e IV). Com a técnica de microarray obteve-se o perfil de expressão de miRNAs das amostras triadas e chegou-se a um conjunto de seis miRNAs candidatos a biomarcadores de prognóstico cirúrgico: miR-92b-3p; miR-1238-3p; miR-1181; miR-636; miR- 1229-3p e miR-486-5p. Em seguida, com a técnica de PCR em tempo real, quantificou-se a expressão destes seis miRNAs e, a partir da otimização de um ponto de corte na escala de expressão, cada miRNA circulante foi apreciado como preditor de resultado cirúrgico. Assim, constatou-se hiperexpressão sanguínea dos seis miRNAs, sem distinção estatística entre os grupos Engel IA e Engel III-IV, hiperexpressão hipocampal do miR-486-5p no grupo Engel IA e hipoexpressão hipocampal do miR-636 nos grupos Engel IA e Engel III-IV. Na análise dos miRNAs circulantes como preditores de sucesso cirúrgico, o miR- 1238-3p exibiu uma sensibilidade de 40,00%, especificidade de 92,86% e acurácia de 65,52%. O conjunto miR-1238/miR1181 mostrou sensibilidade de 46,67%, especificidade de 85,71% e acurácia de 65,52%. O único miRNA circulante sondado como preditor de insucesso cirúrgico, o miR-636, revelou sensibilidade de 21,43%, especificidade de 93,33% e acurácia de 58,62% / A high prevalence, drug resistance and good surgical prognosis are some of the clinical characteristics that cause mesial temporal lobe epilepsy with hippocampal sclerosis (MTLE-HS) to be one of the most important forms of epilepsy. This condition is the model of surgically curable epilepsy, although unfortunately about 10% of the patients exhibit an unsatisfactory surgical outcome. MTLE-HS is associated with extensive changes in the expression profile of hippocampal microRNAs (miRNAs). It has been recently observed that stable miRNAs exist in peripheral blood and in other body fluids which have been proved to be applicable as biomarkers from diagnosis to therapeutic response. On this basis, the present investigation was based on the following question: is it possible to identify molecular signatures by peripheral blood miRNAS that predict the outcome of surgical treatment of MTLE-HS? Molecular biology techniques were used to evaluate blood and hippocampal samples of patients submitted to anterior temporal lobectomy as a consequence of drug-resistant MTLE-HS. The samples were representative of patients with a favorable (Engel IA) and unfavorable (Engel III and IV) surgical outcome. The microarray technique was used to obtain the expression profile of miRNAs in the samples, with a set of six miRNAs being reached as candidate biomarkers for surgical prognosis: miR-92b-3p, miR-1238- 3p, miR-1181, miR-636, miR-1229-3p, and miR-486-5p. Next, real-time PCR was used to quantitate the expression of these six miRNAs and, based on the optimization of a cut-off point on the expression scale, each circulating miRNA was evaluated as surgical outcome predictor. We observed blood hyperexpression of the six miRNAs with no significant difference between the Engel IA and Engel IIIIV groups, hippocampal hyperexpression of miR-486-5p in the Engel IA group, and hippocampal hypoexpression of miR-636 in the Engel IA and Engel III-IV groups. Analysis of circulating miRNAs as predictors of surgical success revealed that miR-1238-3p exhibited 40.00% sensitivity, 92.86% specificity and 65.52% accuracy. The miR-1238/miR1181 set showed 46.67% sensitivity, 85.71% specificity and 65.52% accuracy. The only circulating miRNA evaluated as a predictor of surgical failure, miR-636, showed 21.43% sensitiviy, 93.33% specificity, and 58.62% accuracy

Alta prevalência, farmacorresistência e bom prognóstico cirúrgico são algumas das características clínicas que tornam a epilepsia do lobo temporal mesial com esclerose hipocampal (ELTM-EH) uma das mais importantes formas de epilepsia. Ela é o modelo da epilepsia cirurgicamente curável. Infelizmente, cerca de 10% dos pacientes evoluem com resultado cirúrgico insatisfatório. A ELTM-EH está associada a alterações amplas do perfil de expressão dos microRNAs (miRNAs) do hipocampo. Recentemente, constatou-se a existência de miRNAs estáveis no sangue periférico e em outros fluidos corporais, comprovadamente aplicáveis como biomarcadores, cuja abrangência vai do diagnóstico à resposta terapêutica. Tendo isso em vista, a pesquisa partiu do seguinte questionamento: é possível a identificação, no sangue periférico, de assinaturas moleculares por miRNAs que predigam o resultado do tratamento cirúrgico da ELTM-EH? Por meio de técnicas de biologia molecular, avaliaram-se amostras de sangue e hipocampo de pacientes submetidos à lobectomia temporal anterior em consequência de ELTMEH farmacorresistente. As amostras eram representativas de indivíduos com resultado cirúrgico favorável (Engel IA) e desfavorável (Engel III e IV). Com a técnica de microarray obteve-se o perfil de expressão de miRNAs das amostras triadas e chegou-se a um conjunto de seis miRNAs candidatos a biomarcadores de prognóstico cirúrgico: miR-92b-3p; miR-1238-3p; miR-1181; miR-636; miR- 1229-3p e miR-486-5p. Em seguida, com a técnica de PCR em tempo real, quantificou-se a expressão destes seis miRNAs e, a partir da otimização de um ponto de corte na escala de expressão, cada miRNA circulante foi apreciado como preditor de resultado cirúrgico. Assim, constatou-se hiperexpressão sanguínea dos seis miRNAs, sem distinção estatística entre os grupos Engel IA e Engel III-IV, hiperexpressão hipocampal do miR-486-5p no grupo Engel IA e hipoexpressão hipocampal do miR-636 nos grupos Engel IA e Engel III-IV. Na análise dos miRNAs circulantes como preditores de sucesso cirúrgico, o miR- 1238-3p exibiu uma sensibilidade de 40,00%, especificidade de 92,86% e acurácia de 65,52%. O conjunto miR-1238/miR1181 mostrou sensibilidade de 46,67%, especificidade de 85,71% e acurácia de 65,52%. O único miRNA circulante sondado como preditor de insucesso cirúrgico, o miR-636, revelou sensibilidade de 21,43%, especificidade de 93,33% e acurácia de 58,62% / A high prevalence, drug resistance and good surgical prognosis are some of the clinical characteristics that cause mesial temporal lobe epilepsy with hippocampal sclerosis (MTLE-HS) to be one of the most important forms of epilepsy. This condition is the model of surgically curable epilepsy, although unfortunately about 10% of the patients exhibit an unsatisfactory surgical outcome. MTLE-HS is associated with extensive changes in the expression profile of hippocampal microRNAs (miRNAs). It has been recently observed that stable miRNAs exist in peripheral blood and in other body fluids which have been proved to be applicable as biomarkers from diagnosis to therapeutic response. On this basis, the present investigation was based on the following question: is it possible to identify molecular signatures by peripheral blood miRNAS that predict the outcome of surgical treatment of MTLE-HS? Molecular biology techniques were used to evaluate blood and hippocampal samples of patients submitted to anterior temporal lobectomy as a consequence of drug-resistant MTLE-HS. The samples were representative of patients with a favorable (Engel IA) and unfavorable (Engel III and IV) surgical outcome. The microarray technique was used to obtain the expression profile of miRNAs in the samples, with a set of six miRNAs being reached as candidate biomarkers for surgical prognosis: miR-92b-3p, miR-1238- 3p, miR-1181, miR-636, miR-1229-3p, and miR-486-5p. Next, real-time PCR was used to quantitate the expression of these six miRNAs and, based on the optimization of a cut-off point on the expression scale, each circulating miRNA was evaluated as surgical outcome predictor. We observed blood hyperexpression of the six miRNAs with no significant difference between the Engel IA and Engel IIIIV groups, hippocampal hyperexpression of miR-486-5p in the Engel IA group, and hippocampal hypoexpression of miR-636 in the Engel IA and Engel III-IV groups. Analysis of circulating miRNAs as predictors of surgical success revealed that miR-1238-3p exhibited 40.00% sensitivity, 92.86% specificity and 65.52% accuracy. The miR-1238/miR1181 set showed 46.67% sensitivity, 85.71% specificity and 65.52% accuracy. The only circulating miRNA evaluated as a predictor of surgical failure, miR-636, showed 21.43% sensitiviy, 93.33% specificity, and 58.62% accuracy

Les thérapies moléculaires ciblées ont changé la prise en charge des patients atteints de cancer, et en particulier dans le cancer colorectal (CCR). Il est important d’identifier des biomarqueurs de sensibilité ou de résistance à ces traitements. En premier, la signalisation en aval de l’EGFR au niveau tumoral pourrait conditionner la réponse au cétuximab dans les cancers colorectaux (CCR). Notre premier travail a évalué le niveau d’expression tumorale de phosphoprotéines de signalisation en aval de l’EGFR (p-MEK, p-ERK1/2, p-AKT, p-GSK3b, p-P70S6K) analysés par Bioplex phosphoprotein array chez 42 patients avec un CCR métastatique, traités par anti-EGFR. L’expression de p-P70S6K est plus faible chez les patients répondeurs (p=0,02). La survie sans progression (SSP) est supérieure en cas d’expression faible de p-P70S6K (p=0,0001) et p-MEK (p=0,0006). p-MEK et p-P70S6K ont une expression plus élevée chez les KRAS mutés et apparaissent comme deux marqueurs pronostiques indépendants de KRAS (HR 0,34, p=0,01 et HR 0,42, p=0,03). Ainsi, le niveau d’expression des phosphoprotéines en aval de l’EGFR pourrait prédire la réponse et la SSP dans les CCR traités par anti-EGFR, indépendamment du statut KRAS. Il est difficile dans certain cas d’avoir accès au tissu tumoral. L’ADN circulant (cADN) dans les stades avancés de cancer peut aider à la caractérisation moléculaire des tumeurs, en tant que biopsie. Notre deuxième travail a étudié la faisabilité, la sensibilité et la spécificité d’une technique de spectrométrie de masse (Sequenom) pour détecter des mutations (238 mutations parmi 19 oncogènes) à partir du tissu tumoral et du cADN de 105 patients ayant un cancer avancé. La concentration médiane de cADN était de 17ng/ml de plasma (0,5-1600), soit 3 fois le niveau chez les volontaires sains. En analyse multivariée, la concentration de cADN, l’albumine et l’état général étaient des facteurs prédictifs indépendants de la survie globale des patients. De plus, il existait une concordance élevée des statuts mutationnels (KRAS, BRAF et PIK3CA) entre le tissu tumoral et le cADN dans plusieurs types tumoraux (CCR, sein, mélanome): un taux de concordance de 70% pour le gène KRAS et de 100% pour le gène BRAF ont été retrouvés dans le CCR. Notre Étude suggère que l’analyse du cADN pourrait être un matériel utilisable pour la recherche de mutations, notamment dans le suivi des patients ayant un cancer du colon traités par thérapies ciblées. Notre travail a donc montré l’intérêt de poursuivre l’étude de facteurs moléculaires qui pourraient prédire la réponse ou la résistance à des thérapies ciblées utilisées dans les cancers du colon, au niveau du tissu tumoral (phosphoprotéines) ou au niveau du sang (cADN). / Especially in CRC, it is important to identify molecular targeted therapies biomarkers. First, additional markers of resistance to KRAS mutations could predict resistance to anti-epidermal growth factor receptor (EGFR) antibodies in advanced colorectal cancer (CRC). In our first study, in a series of 42 patients with advanced CRC treated with cetuximab/panitumumab, for whom KRAS status was previously determined, we retrospectively analyzed the intratumor expression of EGFR downstream signaling phosphoproteins of the RAS/MAPK and PI3K/AKT pathways (pERK1/2, pMEK1, pAKT, pP70S6K and pGSK3beta) using Bio-Plex phosphoprotein array. The expression of all the phosphoproteins was higher in KRAS mutated tumors than in WT tumors. The expression of pP70S6K was lower in responders than in nonresponder patients. In multivariate analysis, PFS was shorter for patients with high pMEK1 or pP70S6K expression, independently of KRAS status, as OS for patients with high pP70S6K expression. Our results suggest the importance of EGFR downstream signaling phosphoproteins expression in addition to KRAS status to define the subgroup of patients who will not benefit from anti-EGFR therapy. We hypothesized that circulating plasma DNA (cpDNA) in advanced cancer patients is largely derived from tumor, and can be utilized for tumor mutation sequencing when repeat biopsy is not feasible. In our second study, we utilized the Sequenom MassArray System and OncoCarta panel for somatic mutation profiling. Matched samples, acquired from the same patient but at different time points were evaluated; these comprised formalin-fixed paraffin-embedded (FFPE) archival tumor tissue (primary and/or metastatic) and cpDNA. The feasibility, sensitivity, and specificity of this high-throughput, multiplex mutation detection approach was tested utilizing specimens acquired from 105 patients with solid tumors referred for participation in Phase I trials of molecularly targeted drugs. The median cpDNA concentration was 17 ng/ml (range: 0.5-1600); this was 3-fold higher than in healthy volunteers. In multivariate analyses, cpDNA concentration, albumin, and performance status remained independent predictors of OS. We also observed high detection concordance for critical "hot-spot" mutations (70% for KRAS, 100% for BRAF) in matched cpDNA and archival tumor tissue. This multiplex sequencing assay can be utilized to detectsomatic mutations from plasma in advanced cancer patients, when safe repeat tumor biopsy is not feasible and genomic analysis of archival tumor is deemed insufficient. Our work did show the importance to search for molecular markers to predict response to targeted therapies, both in tumor tissu (phosphoproteins) and in blood (cpDNA).

Un défi de la transcriptomique est d'explorer l'intégralité du répertoire des transcrits normaux et anormaux. Les analyses de GEP (Gene Expression Profiling) basées sur la technologie des puces à ADN sont largement exploitées en cancérologie depuis plusieurs années. Parallèlement, les nouvelles méthodes basées sur le séquençage à haut débit offrent désormais la possibilité de réaliser des analyses précises et sensibles nécessaires à l'étude des cellules normales et cancéreuses. Quelle que soit la méthode, la caractérisation de l'ensemble des transcrits codants et non-codants représente un réel défi biologique pour la recherche de nouveaux marqueurs de diagnostic et de pronostic, et pour la bonne prise en charge des patients. Dans ce travail, j'ai eu l'occasion de traiter deux aspects différents de la biologie qui convergent vers l'identification de transcrits exprimés de manière aberrante dans les leucémies myéloïdes. Le premier aspect a consisté à proposer une sélection de biomarqueurs moléculaires pour la caractérisation de la leucémie myélomonocytaire chronique (LMMC). A partir de l'expression de ces gènes, nous avons développé un score de pronostic qui a permis de définir deux groupes de patients cliniquement distincts. Nous avons ensuite complété notre étude par une caractérisation phénotypique par cytométrie en flux des sous-populations cellulaires aberrantes constituant les lignages mono- et granulocytaires. Une partie de ce travail a été étendue aux leucémies aiguës myéloïdes (LAM) à caryotype normal (CN). L'autre aspect a consisté à participer à la mise en place d'une approche computationnelle intégrée pour caractériser de nouveaux ARNs non annotés et fort probablement non-codants. En explorant des données de Digital Gene Expression (DGE), nous avons quantifié et caractérisé la fraction de ces transcrits dans les régions intergéniques. Nous avons vérifié l'expression de ces nouveaux transcrits dans les tissus normaux et cancéreux en croisant avec d'autres données d'expression, telles que le RNA-Sequencing, et regarder leur conservation et leur expression dans d'autres espèces. / A challenge of transcriptomics is to explore the full repertoire of normal and abnormal transcripts. Gene expression profiling analyses based on microarray technology are widely used in cancer research since many years. Meanwhile, new methods based on high-throughput sequencing methods offers henceforth the possibility to undergo accurate and sensitive analyses necessary for studying normal and cancer cells. Despite the method, the characterization of all coding and non-coding transcripts is a real biological challenge in identifying novel diagnostic and prognostic markers, and for the proper care of patients. In the present work, I had the opportunity to address two different aspects of biology, both convergent toward the identification of aberrantly expressed transcripts in myeloid leukemia. The first aspect was to provide a selection of molecular biomarkers for the characterization of chronic myelomonocytic leukemia (CMML). We developed a gene expression-based prognostic score which identified two clinically distinct groups of patients. We then completed our study with a phenotypic characterization by flow cytometry of aberrant subpopulations constituting the myeloid and granulocytic lineages. A part of this work has been extended to acute myeloid leukemia (AML) patients with normal karyotype. The other aspect was to participate in the implementation of an integrated computational approach in order to characterize novel non annotated RNAs, more likely non-coding. We quantified and characterized the proportion of these transcripts in intergenic regions by exploring Digital Gene Expression (DGE) data. We checked their expression in normal and cancer tissues by crossing with RNA-Seq data, and their conservation and expression in other species.

Les séries sédimentaires, prélevées dans les écosystèmes aquatiques terrestres, constituent des enregistrements ou des archives de l'état d'un système à un instant donné du passé et de son évolution en relation avec la variabilité environnementale naturelle et anthropique. Dans le cadre de cette thèse, l'enregistrement sédimentaire d'un étang piscicole, a été étudié suivant une approche pluridisciplinaire. En particulier, la caractérisation à l'échelle moléculaire et macromoléculaire de la matière organique des sédiments de l'étang de Lansquenet a permis de reconstruire l'histoire de son bassin versant. Basé sur l'utilisation de biomarqueurs et de rapports moléculaires (rapport terrigène/aquatique : TAR(HC), C29/C27(ST), aquatic/macrophyte proxy : Paq, pérylène, syringyle/vanillyle, cinnamyle/vanillyle, acide/aldéhyde des unités syringyles et vanillyle), ce travail a permis d'appréhender, à l'échelle d'un bassin versant, les variations pluriséculaires des sources de la matière organique (terrestre et/ou aquatique, naturelle et/ou anthropique), mais aussi des conditions de dépôt et de préservation, induits par les changements d'usage des sols et les impacts anthropiques. La confrontation de ces résultats avec les données sédimentologiques, minéralogiques et palynologiques a permis de valider la pertinence et la sensibilité de ces biomarqueurs par rapport aux variations environnementales et paléoenvironnementales. Cette étude met ainsi en évidence la succession des usages de ce site depuis un milieu marécageux jusqu'à la création et l'exploitation de l'étang piscicole jalonnée d'épisodes d'assec / The sedimentary series, collected in terrestrial and aquatic ecosystems, constitute records or archives of the state of a system at a given moment of the past and relate its evolution in relation to natural disturbances and anthropogenic pressure. In the following manuscript, the sedimentary record of a fish pond has been studied using a multidisciplinary approach. In particular, the characterization at the molecular and macromolecular scale of the organic matter in sediments of the pond Lansquenet allowed to reconstruct the history of its watershed. On the basis of biomarkers and molecular ratios (terrestrial to aquatic ratio: TAR(HC), C29/C27(ST), aquatic/macrophyte proxy: Paq, perylene, syringyl/vanillyl, cinnamyl/vanillyl, acid/aldehyde of syringyl and vanillyl units), this work has enabled us to understand, at the scale of a watershed, the changes in organic matter origins (terrestrial and/or aquatic, natural and/or anthropogenic) over a period of several centuries. Moreover, the results unraveled the depositional conditions as well as preservation conditions in the sedimentary profile, directly influenced by land use and human activities. The confrontation of organic geochemical data with sedimentological, mineralogical and palynological data was a real benefit and validated the use of a series of organic compounds as relevant and sensitive biomarkers regarding environmental and paleoenvironmental modifications. This study highlighted thus the succession of use of the Lansquenet site from a swampy area to the settlement of a fish pond punctuated by drier periods